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    <title>CardioSHARE demo - Example queries</title>
    <link rel="icon" href="/cardioSHARE/favicon.ico" type="image/x-icon" />
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  	<div id='header'>
      <h1>CardioSHARE demo</h1>
    </div>
    <div id='content'>
      <h2>Example queries</h2>
      
    <ol>
      <li>
        <p class='query-english'> What are all the alternate names for UniProt "P15923"?</p>
        <xmp class='query-sparql'>PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#>
PREFIX uniprot: <http://biordf.net/moby/UniProt/>
SELECT ?name
WHERE {
	uniprot:P15923 pred:hasName ?name
}</xmp>
      </li>
      <li>
        <p class='query-english'> What proteins is Pubmed article 9207092 written about?   What organisms do these proteins belong to?</p>
        <xmp class='query-sparql'>PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#>
PREFIX ont: <http://ontology.dumontierlab.com/>
PREFIX pubmed: <http://biordf.net/moby/PMID/>
SELECT ?protein ?organism
WHERE { 
	pubmed:9207092 ont:isReferenceFor ?protein . 
 	?protein pred:belongsToOrganism ?organism . 
}</xmp>
      </li>
      <li>
        <p class='query-english'> What protein(s) does PDB entry "3SAK" provide a structure  for? What are the amino acid sequences for these proteins?</p>
        <xmp class='query-sparql'>PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#>
PREFIX pdb: <http://biordf.net/moby/PDB/>
SELECT ?protein ?seq
WHERE { 
	pdb:3SAK pred:is3DStructureFor ?protein . 
	?protein pred:hasSequence ?seq .
}</xmp>
      </li>
      <li>
        <p class='query-english'> What pathways does UniProt protein P47989 belong to?</p>
        <xmp class='query-sparql'>PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#>
PREFIX ont: <http://ontology.dumontierlab.com/>
PREFIX uniprot: <http://biordf.net/moby/UniProt/>
SELECT ?gene ?pathway 
WHERE { 
	uniprot:P47989 pred:isEncodedBy ?gene . 
	?gene ont:isParticipantIn ?pathway . 
}</xmp>
      </li>
      <li>
        <p class='query-english'> What GO terms have been used to annotate   proteins that match the keyword "parkinson"?</p>
        <xmp class='query-sparql'>PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#>
PREFIX ont: <http://ontology.dumontierlab.com/>
PREFIX keyword: <http://biordf.net/moby/Global_Keyword/> 
SELECT ?term ?name 
WHERE { 
	keyword:parkinson ont:isTagOf ?protein . 
	?protein pred:hasGOTerm ?term . 
	?term pred:hasTermName ?name 
}</xmp>
      </li>
      <li>
        <p class='query-english'> What genes are involved in the same pathway as KEGG   gene hsa:50616?</p>
        <xmp class='query-sparql'>PREFIX ont: <http://ontology.dumontierlab.com/>
PREFIX kegg: <http://biordf.net/moby/KEGG/hsa:>
SELECT ?pathway ?relatedGene 
WHERE { 
	kegg:50616 ont:isParticipantIn ?pathway . 
	?pathway ont:hasParticipant ?relatedGene .
}</xmp>
      </li>
      <li>
        <p class='query-english'> What genes are involved in both KEGG pathway "hsa00030" and KEGG pathway  "has00500"?</p>
        <xmp class='query-sparql'>PREFIX ont: <http://ontology.dumontierlab.com/>
PREFIX pathway: <http://biordf.net/moby/KEGG_PATHWAY/>
SELECT ?gene 
WHERE { 
	?gene ont:isParticipantIn pathway:hsa00030 . 
	?gene ont:isParticipantIn pathway:hsa00500 .
}</xmp>
      </li>
      <li>
        <p class='query-english'> What genes are involved in KEGG pathway "hsa00232"?   What proteins do those genes code for? What are the   sequences of those proteins?</p>
        <xmp class='query-sparql'>PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#>
PREFIX ont: <http://ontology.dumontierlab.com/>
PREFIX kegg: <http://biordf.net/moby/KEGG_PATHWAY/>
SELECT ?gene ?protein ?seq 
WHERE { 
	kegg:hsa00232 ont:hasParticipant ?gene . 
	?gene pred:encodes ?protein . 
	?protein pred:hasSequence ?seq 
}</xmp>
      </li>
      <li>
        <p class='query-english'> What genes are instances of the class   http://elmonline.ca/dev/simple.owl#simple:CaffeineMetabolismParticipant?</p>
        <xmp class='query-sparql'>PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
PREFIX simple: <http://biordf.net/cardioSHARE/simple.owl#> 
SELECT ?gene 
FROM <http://biordf.net/cardioSHARE/simple.owl> 
WHERE { 
	?gene rdf:type simple:CaffeineMetabolismParticipant 
}</xmp>
      </li>
      <li>
        <p class='query-english'> Show me patients whose creatinine level is increasing   over time, along with their latest BUN and creatinine   levels.</p>
        <xmp class='query-sparql'>PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#> 
PREFIX patient: <http://biordf.net/cardioSHARE/>
SELECT ?patient ?bun ?creat 
FROM <http://biordf.net/cardioSHARE/ElevatedCreatininePatient> 
WHERE { 
	?patient rdf:type patient:ElevatedCreatininePatient . 
	?patient pred:latestBUN ?bun . 
	?patient pred:latestCreatinine ?creat . 
}</xmp>
      </li>
      <li>
        <p class='query-english'>Show me images of the cho snapdragon mutant.</p>
        <xmp class='query-sparql'>PREFIX pred: <http://sadiframework.org/ontologies/service_objects.owl#>
PREFIX moby: <http://biordf.net/moby/DragonDB_Allele/>
SELECT ?image ?desc
WHERE {
	moby:cho pred:visualizedByImage ?image .
	?image pred:hasDescription ?desc
}
</xmp>
      </li>
      <li>
        <p class='query-english'>What are the paralogs of the KEGG CXCL1 gene, and what are their scores</p>
        <xmp class='query-sparql'>PREFIX serv: <http://sadiframework.org/ontologies/service_objects.owl#>
PREFIX kegg: <http://biordf.net/moby/KEGG/hsa:>
SELECT ?gene ?score ?ssdb
WHERE {
    kegg:2919 serv:isParalogOf ?gene .
    ?gene serv:participantInSSDBRecord ?ssdb .
    ?ssdb serv:bitScore  ?score
}
</xmp>
      </li>
      <li>
        <p class='query-english'>Describe the pharmacology of drugs that have atherosclerosis as a known side effect.</p>
        <xmp class='query-sparql'>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX drugbank: <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/>
PREFIX sider: <http://www4.wiwiss.fu-berlin.de/sider/resource/sider/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>

SELECT *
WHERE {
    ?sideEffect sider:sideEffectName "atherosclerosis" .
    ?drug sider:sideEffect ?sideEffect .
    ?drug owl:sameAs ?drugBank .
    ?drugBank drugbank:pharmacology ?pharmacology .
}
</xmp>
      </li>
    </ol>
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